Materials libraries of binary alloy nanoparticles (NPs) are synthesized by combinatorial co-sputter deposition of Cu and Au into the ionic liquid (IL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C(1)C(4)im][Tf2N]), which is contained in a micromachined cavity array substrate. The resulting NPs and NP-suspensions are investigated by transmission electron microscopy (TEM), X-ray diffraction (XRD), UV-Vis measurements (UV-Vis), and attenuated total reflection Fourier transformed infrared (ATR-FTIR) spectroscopy. Whereas the NPs can be directly observed in the IL using TEM, for XRD measurements the NP concentration is too low to lead to satisfactory results. Thus, a new NP isolation process involving capping agents is developed which enables separation of NPs from the IL without changing their size, morphology, composition, and state of aggregation. The results of the NP characterization show that next to the unary Cu and Au NPs, both stoichiometric and non-stoichiometric Cu-Au NPs smaller than 7 nm can be readily obtained. Whereas the size and shape of the alloy NPs change with alloy composition, for a fixed composition the NPs have a small size distribution. The measured lattice constants of all capped NPs show unexpected increased values, which could be related to the NP/surfactant interactions.